annotate pharmcat.xml @ 1:891283e0ee89 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat commit dddf99b20ed9b07334505917f362785e3dace3b9"

<tool id="pharmcat" name="pharmCAT" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
    <description>
        Pharmacogenomics Clinical Annotation Tool
    </description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.7.0</token>
        <token name="@VERSION_SUFFIX@">galaxy0</token>
    </macros>
    <requirements>
        <container type="docker">pgkb/pharmcat:1.7.0</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    ## NAMECALLER FUNCTION
        #if $function_select.function == 'name':
            ln -s '$function_select.input' ./input.vcf &&
            java -cp /pharmcat/pharmcat.jar
            org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher
            -vcf input.vcf
            -json output.json
            -html output.html

    ## PHENOTYPE CALLER FUNCTION
        #else if $function_select.function == 'pheno':
            #if $function_select.method.pheno_function == 'vcf':
                ln -s '$function_select.method.input' ./input.vcf &&
                java -cp /pharmcat/pharmcat.jar
                org.pharmgkb.pharmcat.phenotype.Phenotyper
                -vcf input.vcf
            #else:
                ln -s '$function_select.method.input' ./input.json &&
                java -cp /pharmcat/pharmcat.jar
                org.pharmgkb.pharmcat.phenotype.Phenotyper
                -c input.json
            #end if
            #if $function_select.outside_call:
                -o $function_select.outside_call
            #end if
            -f output.json

    ## REPORTER FUNCTION
        #else if $function_select.function == 'report':
            ln -s '$function_select.input' ./input.json &&
            java -cp /pharmcat/pharmcat.jar
            org.pharmgkb.pharmcat.reporter.Reporter
            -p input.json
            #if $function_select.title:
                -t '$function_select.title'
            #end if
            -j output.json
            -o output.html
    
    ## ALL FUNCTIONS
        #else:
            ln -s '$function_select.input' ./input.vcf &&
            java -jar /pharmcat/pharmcat.jar
            -vcf input.vcf
            -o output
            -f pharmCAT_report_Galaxy
            #if $function_select.outside_call:
                -a $function_select.outside_call
            #end if
            $function_select.json
            $function_select.phenojson
         #end if
    ]]></command>
    <inputs>
        <conditional name="function_select">
            <param name="function" type="select" label="Which function of PharmCAT should be run?">
                <option value="all">Full PharmCAT pipeline</option>
                <option value="name">Only named allele matcher</option>
                <option value="pheno">Only phenotyper</option>
                <option value="report">Only reporter</option>
            </param>
            <when value="all">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                    help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <param name="outside_call" argument="-a" type="data" format="tsv,tabular" label="Gene call TSV file from an outside tool" optional="true"/>
                <param name="json" argument="-j" type="boolean" truevalue="-j" falsevalue="" label="Output reporter JSON report"/>
                <param name="phenojson" argument="-pj" type="boolean" truevalue="-pj" falsevalue="" label="Output phenotyper JSON report"/>
                <!-- <param name="definitions" argument="-na" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="name">
                <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                    help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                <!-- <param name="definitions" argument="-d" type="data" format="list" label="Alternative allele definitions" help="a directory containing allele definitions to use instead of the default packaged allele definitions"/> -->
            </when>
            <when value="pheno">
                <conditional name="method">
                    <param name="pheno_function" type="select" label="Which function of PharmCAT should be run?">
                        <option value="vcf">Run directly from vcf samples</option>
                        <option value="named">Run from the output of the NamedAlleleMatcher</option>
                    </param>
                    <when value="vcf">
                        <param name="input" argument="-vcf" type="data" format="vcf" label="Input vcf file"
                            help="Must be formatted in modified official VCF format as detailed here: https://github.com/PharmGKB/PharmCAT/wiki/VCF-Requirements"/>
                    </when>
                    <when value="named">
                        <param name="input" argument="-c" type="data" format="json" label="Input json file" help="JSON output of the NamedAlleleCaller pharmcat function"/>
                    </when>
                </conditional>
                <param name="outside_call" argument="-o" type="data" format="tabular,tsv" label="Optional TSV of outside caller information" optional="true"/>
            </when>
            <when value="report">
                <param name="input" argument="-p" type="data" format="json" label="JSON call data output from Phenotyper pharmCAT function"/>
                <param name="title" argument="-t" type="text" label="text to add to the report title" optional="true"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="all_out" from_work_dir="output/pharmCAT_report_Galaxy.report.html" format="html" label="Full pharmCAT report on ${on_string}">
            <filter>function_select['function'] == "all"</filter>
        </data>
        <data name="all_pheno" from_work_dir="output/pharmCAT_report_Galaxy.phenotyper.json" format="json" label="pharmCAT Phenotyper report on ${on_string}">
            <filter>function_select['function'] == "all" and function_select["phenojson"]</filter>
        </data>
        <data name="all_out_json" from_work_dir="output/pharmCAT_report_Galaxy.report.json" format="json" label="pharmCAT Reporter JSON on ${on_string}">
            <filter>function_select['function'] == "all" and function_select["json"]</filter>
        </data>
        <data name="namer_html" from_work_dir="output.html" format="html" label="pharmCAT NamedAlleleMatcher html report on ${on_string}">
            <filter>function_select['function'] == "name"</filter>
        </data>
        <data name="namer_json" from_work_dir="output.json" format="json" label="pharmCAT NamedAlleleMatcher json report on ${on_string}">
            <filter>function_select['function'] == "name"</filter>
        </data>
        <data name="pheno_json" from_work_dir="output.json" format="json" label="pharmCAT Phenotyper report on ${on_string}">
            <filter>function_select['function'] == "pheno"</filter>
        </data>
        <data name="report_html" from_work_dir="output.html" format="html" label="pharmCAT Reporter html report on ${on_string}">
            <filter>function_select['function'] == "report"</filter>
        </data>
        <data name="report_json" from_work_dir="output.json" format="json" label="pharmCAT Reporter json report on ${on_string}">
            <filter>function_select['function'] == "report"</filter>
        </data>
    </outputs>
    <tests>
    <!-- ALL FUNCTION -->
        <test expect_num_outputs="3">
            <conditional name="function_select">
                <param name="input" value="test.vcf" ftype="vcf" />
                <param name="outside_call" value="test.tsv" ftype="tabular"/>
                <param name="json" value="-j"/>
                <param name="phenojson" value="-pj"/>
            </conditional>
            <output name="all_out">
                <assert_contents>
                    <has_text text="rs9923231 reference"/>
                    <has_text text="Very high risk of developing hearing loss if administered an aminoglycoside antibiotic."/>
                    <has_text text="CPIC Allele Function, Phenotype and Recommendation"/>
                </assert_contents>
            </output>
            <output name="all_pheno" file="test_1.pheno.json" lines_diff="1"/>
            <output name="all_out_json">
                <assert_contents>
                    <has_text text="Therapeutic range of 200 to 1000 ng/mL has been proposed (PMID 29493375)."/>
                    <has_text text="Activity Score for CYP2D6"/>
                    <has_text text="Implementation Consortium (CPIC) Guideline for CYP2D6 Genotype and Use of Ondansetron and Tropisetron"/>
                </assert_contents>
            </output>
        </test>
    <!-- NAMECALLER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="function" value="name"/>
                <param name="input" value="test.vcf" ftype="vcf"/>
            </conditional>
            <output name="namer_html" file="test_2.html" lines_diff="4" ftype="html" />
            <output name="namer_json" file="test_2.json" lines_diff="2" ftype="json" />
        </test>
    <!-- PHENOTYPER FROM VCF WITH OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>
                <conditional name="method">
                    <param name="pheno_function" value="vcf"/>
                    <param name="input" ftype="vcf" value="test.vcf"/>
                </conditional>
                <param name="outside_call" value="test.tsv"/>
            </conditional>
            <output name="pheno_json" file="test_3.json" lines_diff="1"/>
        </test>
    <!-- PHENOTYPER FROM NAMECALLER AND NO OUTSIDE CALLER-->
        <test expect_num_outputs="1">
            <conditional name="function_select">
                <param name="function" value="pheno"/>
                <conditional name="method">
                    <param name="pheno_function" value="named" />
                    <param name="input" value="test_2.json" ftype="json" />
                </conditional>
            </conditional>
            <output name="pheno_json" file="test_4.json" lines_diff="34"/>
        </test>
    <!-- REPORTER -->
        <test expect_num_outputs="2">
            <conditional name="function_select">
                <param name="input" value="test_3.json" ftype="json"/>
                <param name="function" value="report"/>
                <param name="text" value="test text"/>
            </conditional>
            <output name="report_json">
                <assert_contents>
                    <has_text text="Implication for CYP2C19"/>
                    <has_text text="Lower dose-adjusted trough concentrations of tacrolimus and decreased chance of achieving target tacrolimus concentrations."/>
                    <has_text text="c.1840C\u003eT"/>
                </assert_contents>
            </output>
            <output name="report_html">
                <assert_contents>
                    <has_text text="Two ivacaftor non-responsive alleles"/>
                    <has_text text="rs12979860 reference (C)/rs12979860 reference (C)"/>
                    <has_text text="MT-RNR1: 1555A"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        PharmCAT is a tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.
    ]]></help>
    <citations>
        <citation type="doi" >10.1002/cpt.928</citation>
    </citations>
</tool>